User: llkxiaolan

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llkxiaolan0
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Posts by llkxiaolan

<prev • 21 results • page 2 of 3 • next >
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Answer: A: A puzzle about the results of differential genes
... Sorry, I don't understand. You mean the difference is very small, right? I can't use adj.p.value as a filter condition. Should I use P.Valve? Thanks very much  ...
written 2.2 years ago by llkxiaolan0
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A puzzle about the results of differential genes
... I use the limma package to analyze the data, extract the genetic differences, but in the list of results, adj.p.value are basically the same, which is why, with the same code, analysis of other data, it did not encounter this problem, it is the problem of data.  Here are the results of  data analyz ...
limma written 2.2 years ago by llkxiaolan0
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Comment: C: Some questions about gene annotation
... Thank you very much for your reply. I think I didn't make it clear when I was describing the problem. I used the annotate annotation package to annotate it.  Here's the code I'm using. Can you help me see if there's any problem? The R version I use is 3.4.1.Sorry, I don't know how to upload photos, ...
written 2.2 years ago by llkxiaolan0
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Answer: A: Some questions about gene annotation
... Thank you very much for your reply. I think I didn't make it clear when I was describing the problem. I used the annotate annotation package to annotate it.  Here's the code I'm using. Can you help me see if there's any problem? The R version I use is 3.4.1.Sorry, I don't know how to upload photos, ...
written 2.2 years ago by llkxiaolan0
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Some questions about gene annotation
... I use the limma package for the differential gene analysis, and then use the annotate package for the notes, but why some probe annotation results after the display is not the name of the gene, but NA, what does this mean? Are multiple probes corresponding to one gene?  I am a Chinese student, Engl ...
limma written 2.2 years ago by llkxiaolan0
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Some questions about chip quality control
... When I look at the literature on chip analysis, I've seen many articles that first analyze the quality of the chip. I would like to ask what standards can be used for chip quality analysis?  I know there are scaling factors, β-actin and GAPDH, percent present,NUSE box chart and RLE box chart . But ...
affy written 2.2 years ago by llkxiaolan0 • updated 2.2 years ago by Guido Hooiveld2.5k
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Comment: C: Some doubts about the limma package
... First of all, thank you very much for your reply. Secondly, I've read some of the limma manual. But as a Chinese, I'm a little tired of understanding  ...
written 2.3 years ago by llkxiaolan0
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Comment: C: Some doubts about the limma package
... Thank you very much. After reading a book on the application of R in biology, I know how to do it ...
written 2.3 years ago by llkxiaolan0
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Some doubts about the limma package
... Recently I have been learning limma manual, as a white letter to read the manual completely read mumbo-jumbo, there are many places do not understand, there is no doubts about God, be grateful.  Such is the case : fit <- lmFit(eset.rma[present.probes,], design) fit2 <- contrasts.fit(fit, co ...
affy limma written 2.3 years ago by llkxiaolan0 • updated 2.3 years ago by Aaron Lun25k
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Comment: C: Why can't I use the same R package to get the same conclusions as the author?
... Thank you very much for your reply, and I checked the data later. I think the reason for the different results may be different ways of data preprocessing. Although the number of differential genes is different, I feel that my approach seems to be all right. What do you think?   ...
written 2.3 years ago by llkxiaolan0

Latest awards to llkxiaolan

Popular Question 18 months ago, created a question with more than 1,000 views. For How to annotate the Affymetrix Human Genome U133 Plus 2.0 Array chip
Popular Question 18 months ago, created a question with more than 1,000 views. For How to annotate the [MoGene-2_0-st] Affymetrix Mouse Gene 2.0 ST Array chip

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